CTF#

class CTF(shape, defocus_x, angles=None, opening_axis=None, tilt_axis=None, correct_defocus_gradient=False, sampling_rate=1, acceleration_voltage=300000.0, spherical_aberration=27000000.0, amplitude_contrast=0.07, phase_shift=0, defocus_angle=0, defocus_y=None, flip_phase=True, return_real_fourier=False)[source]#

Bases: object

Representation of a contrast transfer function (CTF) [1].

References

[1]

CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Alexis Rohou and Nikolaus Grigorieff. Journal of Structural Biology 2015.

Attributes

CTF.acceleration_voltage

The acceleration voltage in Volts, defaults to 300e3.

CTF.amplitude_contrast

The amplitude contrast, defaults to 0.07.

CTF.angles

The tilt angles.

CTF.correct_defocus_gradient

Whether to correct defocus gradient, defaults to False.

CTF.defocus_angle

The defocus angle, defaults to 0.

CTF.defocus_y

The defocus value in y direction, defaults to None.

CTF.flip_phase

Whether the returned CTF should be phase-flipped.

CTF.opening_axis

The axis around which the wedge is opened, defaults to None.

CTF.phase_shift

The phase shift, defaults to 0.

CTF.return_real_fourier

Whether to return a format compliant with rfft.

CTF.sampling_rate

The sampling rate, defaults to 1.

CTF.spherical_aberration

The spherical aberration coefficient, defaults to 2.7e7.

CTF.tilt_axis

The axis along which the tilt is applied, defaults to None.

CTF.shape

The shape of the to-be reconstructed volume.

CTF.defocus_x

The defocus value in x direction.

Methods

CTF.from_file(filename)

Initialize CTF from file.

CTF.weight(shape, defocus_x, angles[, ...])

Compute the CTF weight tilt stack.